Differential Gene Expression between Fall- and Spring-Run Chinook Salmon Assessed by Long Serial Analysis of Gene Expression

Of all Pacific salmonids, Chinook salmon Oncorhynchus tshawytscha display the greatest variability in return times to freshwater. The molecular mechanisms of these differential return times have not been well described. Current methods, such as long serial analysis of gene expression (LongSAGE) and microarrays, allow gene expression to be analyzed for thousands of genes simultaneously. To investigate whether differential gene expression is observed between fall- and spring-run Chinook salmon from California's Central Valley, LongSAGE libraries were constructed. Three libraries containing between 25,512 and 29,372 sequenced tags (21 base pairs/tag) were generated using messenger RNA from the brains of adult Chinook salmon returning in fall and spring and from one ocean-caught Chinook salmon. Tags were annotated to genes using complementary DNA libraries from Atlantic salmon Salmo salar and rainbow trout O. mykiss. Differentially expressed genes, as estimated by differences in the number of sequence tags, were found in all pairwise comparisons of libraries (freshwater versus saltwater = 40 genes; fall versus spring = 11 genes: and spawning versus nonspawning = 51 genes). The gene for ependymin, an extracellular glycoprotein involved in behavioral plasticity in fish, exhibited the most differential expression among the three groupings. Reverse transcription polymerase chain reaction analysis verified the differential expression of ependymin between the fall- and spring-run samples. These LongSAGE libraries, the first reported for Chinook salmon, provide a window of the transcriptional changes during Chinook salmon return migration to freshwater and spawning and increase the amount of expressed sequence data.

Parallel Research, Multiple Intellectual Property Right Protection Instruments, and the Correlation among R&D Projects, September 2005

The choice of a research path in attacking scientific and technological problems is a significant component of firms’ R&D strategy. One of the findings of the patent races literature is that, in a competitive market setting, firms’ noncooperative choices of research projects display an excessive degree of correlation, as compared to the socially optimal level. The paper revisits this question in a context in which firms have access to trade secrets, in addition to patents, to assert intellectual property rights (IPR) over their discoveries. We find that the availability of multiple IPR protection instruments can move the paths chosen by firms engaged in an R&D race toward the social optimum.

Imaging for clarification of accusation of treatment error

In the assessment of medical malpractice imaging methods can be used for the documentation of crucial morphological findings which are indicative for or against an iatrogenically caused injury. The clarification of deaths in this context can be usefully supported by postmortem imaging (primarily native computed tomography, angiography, magnetic resonance imaging). Postmortem imaging offers significant additional information compared to an autopsy in the detection of iatrogenic air embolisms and documentation of misplaced medical aids before dissection with an inherent danger of relocation. Additional information is supplied by postmortem imaging in the search for sources of bleeding as well as the documentation of perfusion after cardiovascular surgery. Key criteria for the decision to perform postmortem imaging can be obtained from the necessary preliminary inspection of clinical documentation.

Solid pseudopapillary tumor of the pancreas in children : typical radiological findings and pathological correlation

Introduction : Les tumeurs solides pseudo-papillaires du pancréas (SPT) sont des tumeurs rares, d'étiopathogénie encore incertaine.Le but de notre travail était de décrire les caractéristiques radiologiques des SPT dans le groupe d'âge pédiatrique et d'étudier leur corrélation avec les études anatomopathologiques en vue d'établir un diagnostic.Patients et Méthodes : Nous avons étudié rétrospectivement trois malades pédiatriques pour lesquelles le diagnostic de tumeur solide pseudo-papillaire du pancréas a été porté à l'examen d'une pièce opératoire. Ce groupe comprenait 3 jeunes filles et femmes (âge médian: 13 ans).Résultats : La tumeur a été découverte pendant le bilan de symptômes digestifs non spécifiques. Les examens biologiques n'étaient pas informatifs. Des investigations radiologiques complètes ont été réalisées y compris les ultrasons (US), la tomodensitométrie (CT) et l'imagerie par résonance magnétique (IRM).Celles-ci ont montré de volumineuses lésions nodulaires, peu vascularisées, de compositions habituellement hétérogènes, avec des composantes kystiques et hémorragiques identifiées dans les 3 cas. Un traitement chirurgical a été pratiqué chez toute les patientes. L'étude de la pièce opératoire a montré une tumeur encapsulée dans les 3 cas. Aucune métastase n'a été mise en évidence.Conclusion : Les SPT doivent être considérées dans le diagnostic différentiel des masses pancréatiques pédiatriques, en particulier chez les adolescentes. Certaines caractéristiques radiologiques comme des masses volumineuses bien circonscrites, des lésions hétérogènes avec des zones kystiques et hémorragiques, de plus entourées d'une pseudocapsule fibreuse réactive, suggèrent fortement le diagnostic de SPT. Celui-ci devrait ensuite être confirmé par une biopsie avant que la résection chirurgicale soit effectuée. Chez les enfants, Γ écho graphie abdominale reste la méthode de première intention, suivie par l'IRM comme technique d'imagerie de choix pour évaluer les caractéristiques et l'extension de la lésion, tout en évitant l'exposition des patients aux rayonnements ionisants.

Meta-analysis of gene-level associations for rare variants based on single-variant statistics.

Meta-analysis of genome-wide association studies (GWASs) has led to the discoveries of many common variants associated with complex human diseases. There is a growing recognition that identifying "causal" rare variants also requires large-scale meta-analysis. The fact that association tests with rare variants are performed at the gene level rather than at the variant level poses unprecedented challenges in the meta-analysis. First, different studies may adopt different gene-level tests, so the results are not compatible. Second, gene-level tests require multivariate statistics (i.e., components of the test statistic and their covariance matrix), which are difficult to obtain. To overcome these challenges, we propose to perform gene-level tests for rare variants by combining the results of single-variant analysis (i.e., p values of association tests and effect estimates) from participating studies. This simple strategy is possible because of an insight that multivariate statistics can be recovered from single-variant statistics, together with the correlation matrix of the single-variant test statistics, which can be estimated from one of the participating studies or from a publicly available database. We show both theoretically and numerically that the proposed meta-analysis approach provides accurate control of the type I error and is as powerful as joint analysis of individual participant data. This approach accommodates any disease phenotype and any study design and produces all commonly used gene-level tests. An application to the GWAS summary results of the Genetic Investigation of ANthropometric Traits (GIANT) consortium reveals rare and low-frequency variants associated with human height. The relevant software is freely available.

Error and attack tolerance of layered complex networks.

Many complex systems may be described by not one but a number of complex networks mapped on each other in a multi-layer structure. Because of the interactions and dependencies between these layers, the state of a single layer does not necessarily reflect well the state of the entire system. In this paper we study the robustness of five examples of two-layer complex systems: three real-life data sets in the fields of communication (the Internet), transportation (the European railway system), and biology (the human brain), and two models based on random graphs. In order to cover the whole range of features specific to these systems, we focus on two extreme policies of system's response to failures, no rerouting and full rerouting. Our main finding is that multi-layer systems are much more vulnerable to errors and intentional attacks than they appear from a single layer perspective.

Correlation between depressive symptoms and quality of life in users of psychoactive substances

Objectives: To evaluate the correlation between the presence of depressive symptoms and quality of life in users of psychoactive substances from Psychosocial Attention Centers in Mato Grosso. Method: A cross-sectional analytical study, conducted in Psychosocial Attention Centers, with 109 users. The instruments used were: Medical Outcomes Study 36, Beck Depression Inventory, socio-demographic variables and the use of psychoactive substances. A Tukey analysis and a Spearman correlation were conducted with a significance level of α<0,05. Results: The most affected domains of quality of life were emotional, social and mental health aspects, besides the strong correlation between depressive symptoms and quality of life. Conclusion: The use of psychoactive substances and the presence of symptoms significantly interfere in the life of users, which can compromise the motivation to the treatment, negatively affecting the quality of life in this population.



Geology and correlation of the Mersin mélanges, southern Turkey

Our paper aims to give a thorough description of the infra-ophiolitic melanges associated with the Mersin ophiolite. We propose new regional correlations of the Mersin melanges with other melange-like units or similar series, located both in southern Turkey and adjacent regions. The palaeotectonic implications of the correlations are also discussed. The main results may be summarized as follows: the infra-ophiolitic melange is subdivided into two units, the Upper Cretaceous Sorgun ophiolitic melange and the Ladinian-Carnian Hacialani melange. The Mersin melanges, together with the Antalya and Mamonia domains, are represented by a series of exotic units now found south of the main Taurus range, and are characteristic of the South-Taurides Exotic Units. These melanges clearly show the mixed origin of the different blocks and broken formations. Some components have a Palaeotethyan origin and are characterized by Pennsylvanian and Lower to Middle Permian pelagic and slope deposits. These Palaeotethyan remnants, found exclusively in the Hacialani melange, were reworked as major olistostromes in the Neotethys basin during the Eo-Cimmerian orogenic event. Neotethyan elements are represented by Middle Triassic seamounts and by broken formations containing typical Neotethyan conodont faunas such as Metapolygnathus mersinensis Kozur & Moix and M. primitius s. s., both present in the latest Carnian interval, as well as the occurrence of the middle Norian Epigondolella praeslovakensis Kozur, Masset & Moix. Other elements are clearly derived from the former north Anatolian passive margin and are represented by Huglu-type series including the Upper Triassic syn-rift volcanic event. These sequences attributed to the Huglu-Pindos back-arc ocean were displaced southward during the Late Cretaceous obduction event. The Tauric elements are represented by Eo-Cimmerian flysch-like and molasse sequences intercalated in Neotethyan series. Additionally, some shallow-water blocks might be derived from the Bolkardag para-autochthonous and the Taurus-Beydaglari marginal sequences.

Correlation between the infestation level of Sitophilus zeamais Motschulsky, 1855 (Coleoptera, Curculionidae) and the quality factors of stored corn, Zea mays L. (Poaceae)

This experiment was carried out in order to evaluate the effect of Sitophilus zeamais on physical, physiological and sanitary quality of stored corn. Samples of 500 g of the hybrid OC-705, in three replicates, were conditioned in glasses covered with a screened lid, and kept in chamber at 25±2ºC, 70±5% RH and 12 h of photophase, for 150 days. The infestation levels were 0, 5, 15 and 50 adults/replicate, for the storage periods of 30, 60, 90, 120 and 150 days. The moisture content, classification, weight loss, germination and internal infestation were evaluated monthly. Significant inverse correlations were verified between the number of insects and both the germination and the weight loss; also between the internal infestation and the germination and the standard type. The presence of S. zeamais showed a positive correlation with the weight loss, what means that the internal and external infestations contribute to the reduction of physiological and physical quality of corn seeds. The mean dry matter loss was 0,36%/day, corresponding to a consumption of 0,0001%/insect/month. As the result of those damages, the product suffered reduction of the commercial grade in 30 days, with significant loss in all quality factors.

L'erreur en médecine ambulatoire: comment l'aborder. [Error in ambulatory medicine: how to deal with it?]

Medical errors compromise patient safety in ambulatory practice. These errors must be faced in a framework that reduces to a minimum their consequences for the patients. This approach relies on the implementation of a new culture without stigmatization and where errors are disclosed to the patients; this culture implies the build up of a system for reporting errors associated to an in-depth analysis of the system, looking for root causes and insufficient barriers with the aim to fix them. A useful education tool is the "critical situations" meeting during which physicians are encouraged to openly present adverse events and "near misses". Their analysis, with supportive attitude towards involved staff members, allows to reveal systems failures within the institution or the private practice.

The algebraic equality of two asymptotic tests for the hypothesis that a normal distribution has a specified correlation matrix

It is proved the algebraic equality between Jennrich's (1970) asymptotic$X^2$ test for equality of correlation matrices, and a Wald test statisticderived from Neudecker and Wesselman's (1990) expression of theasymptoticvariance matrix of the sample correlation matrix.